Fix and dependency version bump

Cargo.toml

@@ -13,7 +13,7 @@ repository = "https://github.com/annotation/stam-tools"
 keywords = [ "text-processing", "annotation", "linguistics", "standoff", "nlp"]
 
 [dependencies]
-stam = "0.2.0"
+stam = "0.3.0"
 clap = "3.2.23"
 
 #compile against development version: (doesn't work when building with maturin for pypi)

src/bin/stam/main.rs

@@ -286,15 +286,14 @@ The file contains the following columns:
             if let Some(id) = args.value_of("id") {
                 store = store.with_id(id.to_string());
             }
-        } else {
-            store = annotate(
-                store,
-                &resourcefiles,
-                &setfiles,
-                &storefiles,
-                &annotationfiles,
-            );
         }
+        store = annotate(
+            store,
+            &resourcefiles,
+            &setfiles,
+            &storefiles,
+            &annotationfiles,
+        );
         if !args.is_present("dry-run") {
             store.save().unwrap_or_else(|err| {
                 eprintln!(

src/bin/stam/tag.rs

@@ -59,6 +59,7 @@ fn load_tag_rules(filename: &str) -> Vec<Rule> {
 pub fn tag(store: &mut AnnotationStore, rulefile: &str) {
     let rules = load_tag_rules(rulefile);
     let expressions: Vec<_> = rules.iter().map(|rule| rule.expression.clone()).collect();
+    eprintln!("Loaded {} expressions from {}", rules.len(), rulefile);
     let precompiledset =
         RegexSet::new(expressions.iter().map(|x| x.as_str())).unwrap_or_else(|e| {
             eprintln!("Error in compiling regexset: {}", e);